Published in Genome Res on July 01, 2009
A standard variation file format for human genome sequences. Genome Biol (2010) 7.83
Visualizing genomes: techniques and challenges. Nat Methods (2010) 6.66
PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun (2011) 4.57
seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res (2010) 3.74
The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Res (2014) 3.32
A beginner's guide to eukaryotic genome annotation. Nat Rev Genet (2012) 2.67
Dalliance: interactive genome viewing on the web. Bioinformatics (2011) 2.07
Using GBrowse 2.0 to visualize and share next-generation sequence data. Brief Bioinform (2013) 1.90
Visualizing next-generation sequencing data with JBrowse. Brief Bioinform (2012) 1.70
Web Apollo: a web-based genomic annotation editing platform. Genome Biol (2013) 1.69
SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res (2014) 1.61
Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web. Bioinformatics (2012) 1.49
What does our genome encode? Genome Res (2012) 1.47
The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res (2013) 1.44
Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization. BMC Genomics (2016) 1.43
WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Res (2015) 1.42
The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. Genome Biol (2016) 1.42
ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology. Plant Cell (2017) 1.39
Discovery of McrA, a master regulator of Aspergillus secondary metabolism. Mol Microbiol (2016) 1.37
INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles. PLoS One (2013) 1.36
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics (2012) 1.36
Genome Maps, a new generation genome browser. Nucleic Acids Res (2013) 1.33
An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics (2014) 1.32
Web-based visual analysis for high-throughput genomics. BMC Genomics (2013) 1.31
The Sol Genomics Network (SGN)--from genotype to phenotype to breeding. Nucleic Acids Res (2014) 1.30
DOOR 2.0: presenting operons and their functions through dynamic and integrated views. Nucleic Acids Res (2013) 1.26
Tripal: a construction toolkit for online genome databases. Database (Oxford) (2011) 1.24
Araport: the Arabidopsis information portal. Nucleic Acids Res (2014) 1.23
Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes. BMC Biol (2012) 1.23
G-DOC: a systems medicine platform for personalized oncology. Neoplasia (2011) 1.18
PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. BMC Bioinformatics (2015) 1.15
UP-TORR: online tool for accurate and Up-to-Date annotation of RNAi Reagents. Genetics (2013) 1.14
The i5k Workspace@NAL--enabling genomic data access, visualization and curation of arthropod genomes. Nucleic Acids Res (2014) 1.13
Mouse genome database 2016. Nucleic Acids Res (2015) 1.11
JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol (2016) 1.09
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. Bioinformatics (2012) 1.09
CaPSID: a bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes. BMC Bioinformatics (2012) 1.08
GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR. Database (Oxford) (2011) 1.08
Setting up the JBrowse genome browser. Curr Protoc Bioinformatics (2010) 1.07
Gigwa-Genotype investigator for genome-wide analyses. Gigascience (2016) 1.07
Choosing a genome browser for a Model Organism Database: surveying the maize community. Database (Oxford) (2010) 1.07
CLIPdb: a CLIP-seq database for protein-RNA interactions. BMC Genomics (2015) 1.05
Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii. Plant Cell (2015) 1.04
Integration and visualization of systems biology data in context of the genome. BMC Bioinformatics (2010) 1.02
Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing. MBio (2014) 1.01
An online database for genome information of agricultural plants. Bioinformation (2012) 1.00
Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology. BMC Genomics (2014) 1.00
Developmental progress and current status of the Animal QTLdb. Nucleic Acids Res (2015) 0.98
Comparative analysis and visualization of multiple collinear genomes. BMC Bioinformatics (2012) 0.98
The RNA exosome promotes transcription termination of backtracked RNA polymerase II. Nat Struct Mol Biol (2014) 0.96
RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium. PLoS Pathog (2015) 0.96
ABrowse--a customizable next-generation genome browser framework. BMC Bioinformatics (2012) 0.95
Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system. Proc Natl Acad Sci U S A (2014) 0.94
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res (2013) 0.93
MabsBase: a Mycobacterium abscessus genome and annotation database. PLoS One (2013) 0.92
ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Nucleic Acids Res (2015) 0.92
ChromoZoom: a flexible, fluid, web-based genome browser. Bioinformatics (2012) 0.91
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis. Bioinformatics (2012) 0.91
PlanMine - a mineable resource of planarian biology and biodiversity. Nucleic Acids Res (2015) 0.90
LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Res (2014) 0.90
APADB: a database for alternative polyadenylation and microRNA regulation events. Database (Oxford) (2014) 0.90
iHAT: interactive hierarchical aggregation table for genetic association data. BMC Bioinformatics (2012) 0.90
Quantitative bacterial transcriptomics with RNA-seq. Curr Opin Microbiol (2014) 0.90
The coffee genome hub: a resource for coffee genomes. Nucleic Acids Res (2014) 0.89
RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data. Nucleic Acids Res (2015) 0.88
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse. Nucleic Acids Res (2016) 0.87
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput Biol (2015) 0.87
Sublethal concentrations of carbapenems alter cell morphology and genomic expression of Klebsiella pneumoniae biofilms. Antimicrob Agents Chemother (2015) 0.87
RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA. RNA (2011) 0.87
Phase variation of poly-N-acetylglucosamine expression in Staphylococcus aureus. PLoS Pathog (2014) 0.86
The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. Plant Cell (2017) 0.86
Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic Acids Res (2016) 0.86
NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes. Nucleic Acids Res (2013) 0.86
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. Gigascience (2015) 0.85
MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data. Nucleic Acids Res (2014) 0.85
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data. BMC Genomics (2012) 0.85
Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. Nucleic Acids Res (2015) 0.85
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. Nucleic Acids Res (2016) 0.85
Host genome integration and giant virus-induced reactivation of the virophage mavirus. Nature (2016) 0.84
GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications. Bioinformatics (2015) 0.84
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. Nucleic Acids Res (2015) 0.84
afterParty: turning raw transcriptomes into permanent resources. BMC Bioinformatics (2013) 0.83
Information Commons for Rice (IC4R). Nucleic Acids Res (2015) 0.83
BLASTPLOT: a PERL module to plot next generation sequencing NCBI-BLAST results. Source Code Biol Med (2014) 0.83
COV2HTML: a visualization and analysis tool of bacterial next generation sequencing (NGS) data for postgenomics life scientists. OMICS (2014) 0.83
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. Nucleic Acids Res (2015) 0.82
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context. J Clin Bioinforma (2011) 0.82
piRNAQuest: searching the piRNAome for silencers. BMC Genomics (2014) 0.82
Genome annotation of Burkholderia sp. SJ98 with special focus on chemotaxis genes. PLoS One (2013) 0.82
Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian. BMC Genomics (2014) 0.82
The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data. Nucleic Acids Res (2016) 0.81
Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop. Nat Commun (2015) 0.81
LncRBase: an enriched resource for lncRNA information. PLoS One (2014) 0.81
DBSecSys: a database of Burkholderia mallei secretion systems. BMC Bioinformatics (2014) 0.81
dictyBase 2015: Expanding data and annotations in a new software environment. Genesis (2015) 0.81
HPVbase--a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas. Sci Rep (2015) 0.80
Mouse Genome Database: From sequence to phenotypes and disease models. Genesis (2015) 0.80
JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison. BMC Bioinformatics (2013) 0.80
ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome. BMC Genomics (2010) 0.80
Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes. BMC Genomics (2015) 0.79
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
The human genome browser at UCSC. Genome Res (2002) 168.23
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
The generic genome browser: a building block for a model organism system database. Genome Res (2002) 42.64
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell (2008) 32.65
FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res (2008) 12.15
The UCSC Genome Browser Database: update 2009. Nucleic Acids Res (2008) 10.31
A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics (2007) 8.47
Genome re-annotation: a wiki solution? Genome Biol (2007) 4.61
Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. Bioinformatics (2007) 4.29
The Ensembl Web site: mechanics of a genome browser. Genome Res (2004) 4.10
The UCSC Cancer Genomics Browser. Nat Methods (2009) 3.08
X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis. Nucleic Acids Res (2007) 2.69
Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics (2009) 1.73
Understanding genome browsing. Nat Biotechnol (2009) 1.55
Evolving from bioinformatics in-the-small to bioinformatics in-the-large. OMICS (2003) 1.14
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol (2007) 35.41
International network of cancer genome projects. Nature (2010) 20.35
The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol (2005) 18.20
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet (2010) 16.96
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
AmiGO: online access to ontology and annotation data. Bioinformatics (2008) 10.77
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol (2002) 8.59
Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature (2012) 8.31
WormBase: better software, richer content. Nucleic Acids Res (2006) 6.78
A promoter-level mammalian expression atlas. Nature (2014) 6.25
The International HapMap Project Web site. Genome Res (2005) 5.96
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res (2013) 5.66
WormBase: a cross-species database for comparative genomics. Nucleic Acids Res (2003) 5.28
WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20
Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol (2009) 5.17
WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res (2004) 4.14
WormBase: new content and better access. Nucleic Acids Res (2006) 4.01
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res (2005) 3.82
WormBase 2007. Nucleic Acids Res (2007) 3.69
Logical development of the cell ontology. BMC Bioinformatics (2011) 3.68
Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. PLoS Genet (2012) 3.21
Gramene, a tool for grass genomics. Plant Physiol (2002) 3.14
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. BMC Bioinformatics (2010) 3.10
FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods (2010) 2.71
Arabidopsis reactome: a foundation knowledgebase for plant systems biology. Plant Cell (2008) 2.50
Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res (2013) 2.24
modMine: flexible access to modENCODE data. Nucleic Acids Res (2011) 2.18
The SNP Consortium website: past, present and future. Nucleic Acids Res (2003) 2.08
Human genome: end of the beginning. Nature (2004) 2.06
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol (2006) 2.03
The Release 5.1 annotation of Drosophila melanogaster heterochromatin. Science (2007) 1.95
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (2015) 1.91
The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics (2013) 1.76
RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73
A genome-wide association search for type 2 diabetes genes in African Americans. PLoS One (2012) 1.72
Ontologies as integrative tools for plant science. Am J Bot (2012) 1.71
WormBook: the online review of Caenorhabditis elegans biology. Nucleic Acids Res (2006) 1.71
Web Apollo: a web-based genomic annotation editing platform. Genome Biol (2013) 1.69
The Reactome BioMart. Database (Oxford) (2011) 1.66
The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol (2012) 1.65
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput Biol (2012) 1.65
Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods (2013) 1.64
Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol (2015) 1.58
Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans. Genome Res (2006) 1.56
nGASP--the nematode genome annotation assessment project. BMC Bioinformatics (2008) 1.52
Feasibility of real time next generation sequencing of cancer genes linked to drug response: results from a clinical trial. Int J Cancer (2012) 1.49
Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform (2010) 1.48
WormBase as an integrated platform for the C. elegans ORFeome. Genome Res (2004) 1.47
MouseFinder: Candidate disease genes from mouse phenotype data. Hum Mutat (2012) 1.41
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. Database (Oxford) (2011) 1.39
Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. Dis Model Mech (2012) 1.39
GMODWeb: a web framework for the Generic Model Organism Database. Genome Biol (2008) 1.38
Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biol (2008) 1.30
XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics (2006) 1.29
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. BMC Genomics (2013) 1.27
Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics. Genome Biol (2006) 1.25
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. J Biomed Semantics (2013) 1.22
A unified anatomy ontology of the vertebrate skeletal system. PLoS One (2012) 1.22
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. BMC Genomics (2013) 1.18
Identification of a nematode chemosensory gene family. Proc Natl Acad Sci U S A (2004) 1.14
Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer. Mol Cell Proteomics (2012) 1.08
Setting up the JBrowse genome browser. Curr Protoc Bioinformatics (2010) 1.07
Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol (2014) 1.07
Rotaviruses interact with alpha4beta7 and alpha4beta1 integrins by binding the same integrin domains as natural ligands. J Gen Virol (2005) 1.05
A knowledge based approach to matching human neurodegenerative disease and animal models. Front Neuroinform (2013) 1.04
A strategy for building neuroanatomy ontologies. Bioinformatics (2012) 1.03
Localizing triplet periodicity in DNA and cDNA sequences. BMC Bioinformatics (2010) 0.99
Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants. Int J Cancer (2013) 0.87
Colorstock, SScolor, Ratón: RNA alignment visualization tools. Bioinformatics (2008) 0.86
Mapping of conformational epitopes on capsid protein VP2 of infectious bursal disease virus by fd-tet phage display. J Virol Methods (2003) 0.82
WormBase: methods for data mining and comparative genomics. Methods Mol Biol (2006) 0.82
Exome sequencing identifies nonsegregating nonsense ATM and PALB2 variants in familial pancreatic cancer. Hum Genomics (2013) 0.82
Evolutionary modeling and prediction of non-coding RNAs in Drosophila. PLoS One (2009) 0.81
Gallus GBrowse: a unified genomic database for the chicken. Nucleic Acids Res (2007) 0.81
Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinformatics (2013) 0.77
Historian: accurate reconstruction of ancestral sequences and evolutionary rates. Bioinformatics (2017) 0.75
Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process. BMC Evol Biol (2013) 0.75
Erratum: A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns. Nature (2016) 0.75
INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Pac Symp Biocomput (2016) 0.75
KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. bioRxiv (2020) 0.75
Identification of crucial residues of conformational epitopes on VP2 protein of infectious bursal disease virus by phage display. J Virol Methods (2003) 0.75